Additional file 3 of DNA methylation profiles of bronchoscopic biopsies for the diagnosis of lung cancer

Additional file 3. Fig. S2: Validation of DNA methylation values collected by HumanMethylation450 BeadChip (HM450 BC) using bisulfite sequencing (BSPS). For verifying results obtained by array analysis, 13 CpG loci were selected and BSPS assays were designed. These loci were subsequently analyzed in both malignant and benign samples of surgical and biopsy specimens. Overall 608 BSPS reactions were performed for HM450 BC data verification. Afterwards, BSPS data was correlated with data obtained from HM450 BC analysis by determining the Pearson’s correlation coefficient. The results of the overall analysis as well as the analysis of four specimens’ subgroups are shown. Additional BSPS assays succeeded to validate loci differentially methylated between SQC and AC as determined by HM450 BC analysis (data not shown). Data sets from the following CpG loci were included: cg04415798, cg23322933, cg18103859, cg05877497 (24 surgical specimens and 24 biopsy samples: 12 tumors, 12 controls each); cg22620090, cg06809252 (24 surgical specimens: 12 tumors, 12 controls and 22 biopsy samples: 11 tumors, 11 controls), cg13588800, cg20052718, cg17839237, cg24446548 (34 surgical specimens: 17 tumors, 17 controls and 24 biopsy samples: 12 tumors, 12 controls), cg02391713 (24 surgical specimens: 12 tumors, 12 controls), cg00240432 and cg14782672 (34 surgical specimens: 17 tumors, 17 controls).